Dasari Surendra, Theis Jason D, Vrana Julie A, Meureta Oana M, Quint Patrick S, Muppa Prasuna, Zenka Roman M, Tschumper Renee C, Jelinek Diane F, Davila Jaime I, Sarangi Vivekananda, Kurtin Paul J, Dogan Ahmet
†Department of Health Sciences Research, ‡Department of Laboratory Medicine and Pathology, §Information Technology Administration, and ∥Department of Immunology and Division of Hematology, Mayo Clinic, 200 First Street SW, Rochester, Minnesota 55905, United States.
J Proteome Res. 2015 Apr 3;14(4):1957-67. doi: 10.1021/acs.jproteome.5b00015. Epub 2015 Mar 20.
Immunoglobulin light chain (LC) amyloidosis (AL) is caused by deposition of clonal LCs produced by an underlying plasma cell neoplasm. The clonotypic LC sequences are unique to each patient, and they cannot be reliably detected by either immunoassays or standard proteomic workflows that target the constant regions of LCs. We addressed this issue by developing a novel sequence template-based workflow to detect LC variable (LCV) region peptides directly from AL amyloid deposits. The workflow was implemented in a CAP/CLIA compliant clinical laboratory dedicated to proteomic subtyping of amyloid deposits extracted from either formalin-fixed paraffin-embedded tissues or subcutaneous fat aspirates. We evaluated the performance of the workflow on a validation cohort of 30 AL patients, whose amyloidogenic clone was identified using a novel proteogenomics method, and 30 controls. The recall and negative predictive values of the workflow, when identifying the gene family of the AL clone, were 93 and 98%, respectively. Application of the workflow on a clinical cohort of 500 AL amyloidosis samples highlighted a bias in the LCV gene families used by the AL clones. We also detected similarity between AL clones deposited in multiple organs of systemic AL patients. In summary, AL proteomic data sets are rich in LCV region peptides of potential clinical significance that are recoverable with advanced bioinformatics.
免疫球蛋白轻链（LC）淀粉样变性（AL）由潜在浆细胞瘤产生的克隆性轻链沉积所致。克隆型轻链序列对每位患者而言都是独特的，通过针对轻链恒定区的免疫测定或标准蛋白质组学工作流程无法可靠地检测到这些序列。我们通过开发一种基于新型序列模板的工作流程来直接从AL淀粉样沉积物中检测轻链可变（LCV）区肽段，解决了这一问题。该工作流程在一个符合CAP/CLIA标准的临床实验室中实施，该实验室专门用于对从福尔马林固定石蜡包埋组织或皮下脂肪抽吸物中提取的淀粉样沉积物进行蛋白质组学分型。我们在一个由30例AL患者组成的验证队列以及30例对照中评估了该工作流程的性能，这些AL患者的淀粉样蛋白生成克隆是使用一种新型蛋白质基因组学方法鉴定出来的。在鉴定AL克隆的基因家族时，该工作流程的召回率和阴性预测值分别为93%和98%。将该工作流程应用于一个包含500例AL淀粉样变性样本的临床队列，突出显示了AL克隆所使用的LCV基因家族存在偏差。我们还检测到系统性AL患者多个器官中沉积的AL克隆之间存在相似性。总之，AL蛋白质组数据集富含具有潜在临床意义的LCV区肽段，可通过先进的生物信息学方法进行回收。
